Introduction

The purpose of this forum is to introduce notable papers and books published by you and other persons. The work can be new or old, but it should be of wide interest and high quality. A brief comment on the significance of the work should be attached. The current categories of the subjects are (1) adaptation, (2) behavioral evolution, (3) dosage compensation, (4) evo-devo, (5) gene evolution, (6) genomic evolution, (7) molecular phylogeny, (8) natural selection, (9) phenotypic evolution, (10) sensory receptors, (11) sex chromosomes, (12) sex determination, (13) speciation, (14) symbiosis and evolution, and (15) horizontal gene transfer. However, new categories can be added if necessary. Emphasis will be given on the biological work rather than on the mathematical. Any person may post a paper by sending it to one of the editors listed below. We also welcome your comments on posted work, but we moderate all the comments to control spam. This forum is primarily for scientific discussion and to construct a database for good molecular evolution papers.

Friday, March 14, 2014

Horizontal Gene Transfer Takes a Turn: Expansins from Plants to their Bacterial and Eukaryotic Parasites

Genetic material is inherited from parents
to offspring and this process is known as vertical transmission. However
genetic material can be transferred form one organism to another in a non-genealogical
fashion. Such type of transmission is defined as horizontal transmission or gene
transfer (HGT) (1). Although mechanisms for the transfer of genetic material
between organisms were known from the early years of molecular biology and
genetics research, and the theoretical potential of cross-species gene transfer
in evolution was proposed in the 1980s, the concept of HGT emerged in the 1990s
(2). It was invoked as an alternative explanation for rarely observed incongruent
phylogenetic relationships between species (2). However, the recent
availability of genome sequence information and the thorough study of multiple pro-
and eukaryotic genomes has revealed that HGT is pervasive and powerful among
microbes (1,2,3). Additionally, more recent studies have shown that HGT is also
evident between animals and bacteria, with the bacteria being the donor species
(4,5). In plants, HGT has been relatively well documented, and in most cases
involves the transfer of genetic material from a parasite to its host plant. Yet,
HGTs with the plant species being the donor have rarely been documented.

Recently Nikolaidis et al (6) reported a
rare case of HGT from plants to multiple plant parasites or free living microorganisms.
Specifically, they found that members of the plant expansin gene family, which
code for plant cell-wall loosening proteins and are comprised of two distinct
protein domains D1 and D2, were transferred from plants to bacteria, fungi, and
unicellular eukaryotes (amoebozoa).

Having previously established that the
bacterial protein EXLX1 from Bacillus subtilis
is structurally and functionally very similar to plant expansins (7,8,9),
Nikolaidis et al investigated the evolution of the expansin family in-depth. To
do so they used the bacterial EXLX1 sequence as their primary-sequence database
interrogator. Like expansins, EXLX1
protein contains two domains, D1 and D2, which are tightly packed structurally
with a conserved open surface spanning both of them (Figure 1a,b). To ensure
that the resulted raw sequence alignments of their exhaustive similarity
searches are not random hits, the authors employed a set of established strict search
criteria. Remarkably, they identified numerous
sequences from bacteria, fungi, and amoebozoa that align to both EXLX1 domains
and therefore may share ancestry with it. If so, the identified sequences are EXLX1
homologs. By employing proven phylogenetic tools and methods, as well as
protein domain and fold recognition programs, the authors confirmed that all
identified proteins contain both expansin domains, and showed that the
predicted protein structures are very similar to both B. subtilis EXLX1 and plant expansins, further supporting the homology
inference (Figures 1 and 2).

Figure 1. The EXLX1 homologs
are predicted to contain two domains, fold similarly to the Zea mays EXPB1 (a) and the B. subtilis EXLX1 (b), and contain a
conserved long hydrophobic surface. (c, d) structural alignments of the
three-dimensional models of the EXLX1 homologs from Ralstonia and Erwinia
with the EXLX1structure. Surface (e) and ribbon (f) representations of the
EXLX1 structure are colored according to conservation in 70 EXP domain
sequences from bacteria and fungi (blue to red with increasing
conservation). From Nikolaidis et al. (2014) (6).

Figure 2. The Bacillus subtilis EXLX1protein has many
homologs in bacteria, fungi, and amoebozoa. (a) Phylogenetic
relationships of representative B. subtilisEXLX1 homologs. Two
different phylogenetic methods (NJ and ML) were used with gamma-distributed
distances from the WAG substitution model with α = 1.72.
Alignment gaps were excluded and the total number of sites used to construct
the trees was 176. The numbers at the nodes are bootstrap values (NJ/ML). The
biology of each species is shown with different symbols next to the species
name. Species names abbreviations are given in supplementary table S1, Supplementary
Material online. Only sequences producing BLAST hits with E-values lower
than 10−4 and query coverage higher than 80% were used for the
construction of these trees (b). Many EXLX1homologs contain additional
domains. The domain organization of the EXLX1 homologs was identified using the
Conserved Domains Database (CDD) database from NCBI coupled to fold recognition
analysis. We define as expansin the domain that contains both D1 and D2 domains
according to the EXLX1structure (Kerff et al. 2008; Georgelis et al. 2013).
From Nikolaidis et al. (2014) (6).

However, sequence similarity is not sufficient for
showing the genetic-material-transmission type—vertical or horizontal. Five significant
observations led the authors to support the HGT type: a) the sporadic
distribution of organisms harboring expansin homologs, b) the biological
features of these organisms –plant pathogens, soil inhabitants, or cellulose
producers, c) the incongruence between the phylogenetic tree derived from EXLX1
and its homologs and the established bacterial or fungal species tree, d) the
fusion of additional and shared protein domains (cellulase GH5 or
carbohydrate-binding modules) in several EXLX1 homologs, and e) the functional
similarities between microbial and plant expansins, especially the lack of
catalytic activity. The latter observation argues against convergence (independent
fusion of D1 and D2 domains) because such a scenario would require the biochemically
and evolutionarily improbable independent loss and gain of the same amino acid
residues in multiple distant phyla.

Relaxing the criteria of their sequence similarity
searches, the authors also examined whether sequences similar to each one of
the two expansin domains exist. Their results were positive for both domains. Applying
their phylogenetic/protein fold recognition methodology to the sequences
similar only to the second expansin domain (D2), the authors showed that the
fungal swollenin protein family is homologous to expansins. Swollenin proteins
are composed of two domains, too. Interestingly, although their N-terminal D1
domain contains many conserved insertions and therefore bears very low similarity
with the expansin D1 domain, the folding patterns are very similar.

Regarding the timing of the expansin HGT, the lack of
any differences in parametric measures such as GC-content, amino acid or
nucleotide usage, etc., in the EXLX1 homologs allowed the authors to conclude
it was not recent. Two additional observations augmented this conclusion.
First, the phylogenetic patterns revealed that the HGT of expansins was
followed by vertical transfers during certain fungal or amoebozoan species
evolution. Second, several bacterial and fungal distant species contain
expansin genes fused with cellulose GH5 and carbohydrate-binding domains,
respectively. According to the authors’ phylogenetic analysis these extra
domains were most likely acquired independently by convergence. Therefore the
HGT of expansins from plants to other organisms preceded the long-lasting and
slow events of convergence and speciation. Hence it must be ancient.

Regarding the origin of the expansin gene family, the
authors, following a reductio ad absurdum
argumentation, favor the scenario of a single origin in the common ancestor of
plants and subsequent horizontal transmission to non-plant species. The patchy distribution
of EXLX1 homologs in a small percentage of the tested bacterial (128/4,281 or
3%) and fungal (28 /543 or 5.2%) genomes argues against a single origin in
bacteria and subsequent vertical transmission, since such a scenario demands
the absurd assumption of multiple independent gene losses.Additionally, the authors’ previously
reported functional similarities between plant and microbial expansins (8,9) argues
against convergence, and therefore augments the single origin scenario.

Nikolaidis et al., offer a long list of logical and
tightly woven arguments for the HGT scenario of non-plant expansins. However they do admit
the difficulty of proving it beyond
reasonable doubt. Another task—yet harder in the case of expansins—is to determine
precisely the donor and recipient species, as well as its mechanism and timing.
As more genomes are being sequenced we will probably be able to define at least
a plant lineage that contributed its expansins to its intimately associated parasites.
If so, then investigation for the potential mechanisms of HGT will be somehow
eased.A current plausible such
mechanism includes a plasmid-mediated transfer (10).

Besides the mechanism and timing of expansins’ HGT,
their adaptive significance for the recipient species is of essence. Experimental
studies on the physiological role of non-plant expansins have started to shed
light on this topic. The authors report several such studies and propose that the
HGT of expansin proteins in plant-interacting microbes contributed new or
alternative tools for colonization or infection. The latter hypothesis implies
an adaptive advantage for the plant-infecting organisms and together with the
results of other reports on the role of HGT to the emergence of new diseases
suggests that the observed rarity of HGT is not indicative of its importance in
organismal evolution.